Display options
Cite
Carlin D, Kosnicki K, Garamszegi S, et al. A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Res. 2017;6:784doi: 10.12688/f1000research.11616.1.
Carlin, D., Kosnicki, K., Garamszegi, S., Ideker, T., Thorvaldsdóttir, H., Reich, M., & Mesirov, J. (2017). A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Research, 6784. https://doi.org/10.12688/f1000research.11616.1
Carlin, Daniel, et al. "A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression." F1000Research vol. 6 (2017): 784. doi: https://doi.org/10.12688/f1000research.11616.1
Carlin D, Kosnicki K, Garamszegi S, Ideker T, Thorvaldsdóttir H, Reich M, Mesirov J. A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Res. 2017 Jun 06;6:784. doi: 10.12688/f1000research.11616.1. eCollection 2017. PMID: 29487738; PMCID: PMC5806050.
Copy Download .nbib Format: NLM
Share it on

F1000Res. 2017 Jun 06;6:784. doi: 10.12688/f1000research.11616.1. eCollection 2017.

A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression.

F1000Research

Daniel Carlin, Kassi Kosnicki, Sara Garamszegi, Trey Ideker, Helga Thorvaldsdóttir, Michael Reich, Jill Mesirov

Affiliations

  1. The University of California, San Diego School of Medicine, 500 Gilman Dr, La Jolla, CA, 92093, USA.
  2. Broad Institute, Cambridge, MA, 02142, USA.
  3. Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA.

PMID: 29487738 PMCID: PMC5806050 DOI: 10.12688/f1000research.11616.1

Abstract

One commonly performed bioinformatics task is to infer functional regulation of transcription factors by observing differential expression under a knockout, and integrating DNA binding information of that transcription factor.   However, until now, this this task has required dedicated bioinformatics support to perform the necessary data integration. GenomeSpace provides a protocol, or "recipe", and a user interface with inter-operating software tools to identifying protein occupancies along the genome from a ChIP-seq experiment and associated differentially regulated genes from an RNA-Seq experiment. By integrating RNA-Seq and ChIP-seq analyses, a user is easily able to associate differing expression phenotypes with changing epigenetic landscapes.

Keywords: ChIP-seq; RNA-Seq; data integration; differential expression; epigenetics; histone modification; regulation; transcription factor

Conflict of interest statement

Competing interests: No competing interests were disclosed.

Publication Types